CNV.detailplot_wrap: CNV.detailplot_wrap

In conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Description

Create CNV plot for all detail regions.

Usage

CNV.detailplot_wrap(object, ...)

## S4 method for signature 'CNV.analysis'
CNV.detailplot_wrap(object, set_par = TRUE,
  main = NULL, ...)

Arguments

object	CNV.analysis object.
...	Additional paramters supplied to CNV.detailplot.
set_par	logical. Use recommended graphical parameters for oma and mar? Defaults to TRUE. Original parameters are restored afterwards.
main	character. Title of the plot. Defaults to sample name.

Details

This method is a wrapper of the CNV.detailplot method to plot all detail regions.

Value

NULL.

Author(s)

Volker Hovestadt [e-mail]

Examples

# prepare
library(minfiData)
data(MsetEx)
d <- CNV.load(MsetEx)
data(detail_regions)
anno <- CNV.create_anno(detail_regions = detail_regions)

# create/modify object
x <- CNV.segment(CNV.detail(CNV.bin(CNV.fit(query = d['GroupB_1'],
    ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno))))

# output plots
CNV.genomeplot(x)
CNV.genomeplot(x, chr = 'chr6')
CNV.detailplot(x, name = 'PTEN')
CNV.detailplot_wrap(x)

# output text files
CNV.write(x, what = 'segments')
CNV.write(x, what = 'detail')
CNV.write(x, what = 'bins')
CNV.write(x, what = 'probes')

conumee documentation built on Nov. 8, 2020, 6 p.m.